Database Authors
Pallavi Subhraveti1, Peter Midford1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Oct-2019 from the annotated genome of Acinetobacter radioresistens DD78, as obtained from RefSeq (see the RefSeq entry for the authors of the original genome sequence). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 23.0) [Karp16, Karp11] using MetaCyc version 23.1 [Caspi20]. It has not undergone any manual curation or review, and may contain errors. Development of this PGDB was supported by grant GM080746 from the National Institutes of Health.
Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_CP0380222,8212,671102483,009,347RefSeq:NZ_CP038022
pAR1816801388,584RefSeq:NZ_CP038023
pAR3897001980,103RefSeq:NZ_CP038025
pAR280710969,207RefSeq:NZ_CP038024
Total:3,0712,880102893,247,241
Ortholog data available?Yes
Database Contents
Genes3,071
Pathways226
Enzymatic Reactions1,374
Transport Reactions66
Polypeptides2,882
Protein Complexes34
Enzymes667
Transporters268
Compounds1,200
Transcription Units2,065
tRNAs77
Protein Features3,603
GO Terms27
Database Version29.0
Synonyms Acinetobacter genomosp. 12
Acinetobacter genomospecies 12
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter radioresistens
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN11179230
NCBI BioProjectPRJNA224116
NCBI-Taxonomy40216
Environmentsoil
Geographic LocationChile
Collection Date2008-12-31/2008-11-30
Annotation ProviderNCBI RefSeq
Annotation Date2019-05-22
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.8
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2019). "The MetaCyc database of metabolic pathways and enzymes-a 2019 update." Nucleic Acids Res. PMID: 31586394

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Karp16: Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R (2016). "Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform 17(5);877-90. PMID: 26454094

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